Incidental Mutation 'R0681:Rfx5'
ID |
60955 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Rfx5
|
Ensembl Gene |
ENSMUSG00000005774 |
Gene Name |
regulatory factor X, 5 (influences HLA class II expression) |
Synonyms |
|
MMRRC Submission |
038866-MU
|
Accession Numbers |
|
Essential gene? |
Possibly non essential
(E-score: 0.274)
|
Stock # |
R0681 (G1)
|
Quality Score |
95 |
Status
|
Validated
|
Chromosome |
3 |
Chromosomal Location |
94861355-94868685 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
C to T
at 94863666 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Threonine to Isoleucine
at position 105
(T105I)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000118586
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000029772]
[ENSMUST00000107253]
[ENSMUST00000107254]
[ENSMUST00000107255]
[ENSMUST00000107260]
[ENSMUST00000132393]
[ENSMUST00000137088]
[ENSMUST00000142311]
[ENSMUST00000145031]
[ENSMUST00000147237]
[ENSMUST00000145472]
[ENSMUST00000152869]
[ENSMUST00000140331]
[ENSMUST00000144132]
|
AlphaFold |
Q9JL61 |
Predicted Effect |
probably damaging
Transcript: ENSMUST00000029772
AA Change: T105I
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000029772 Gene: ENSMUSG00000005774 AA Change: T105I
Domain | Start | End | E-Value | Type |
Pfam:RFX_DNA_binding
|
84 |
169 |
7.2e-33 |
PFAM |
RFX5_DNA_bdg
|
438 |
656 |
4.29e-130 |
SMART |
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000107253
AA Change: T105I
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000102874 Gene: ENSMUSG00000005774 AA Change: T105I
Domain | Start | End | E-Value | Type |
Pfam:RFX_DNA_binding
|
84 |
169 |
1.8e-33 |
PFAM |
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000107254
AA Change: T105I
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000102875 Gene: ENSMUSG00000005774 AA Change: T105I
Domain | Start | End | E-Value | Type |
Pfam:RFX_DNA_binding
|
84 |
169 |
1.8e-33 |
PFAM |
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000107255
AA Change: T105I
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000102876 Gene: ENSMUSG00000005774 AA Change: T105I
Domain | Start | End | E-Value | Type |
Pfam:RFX_DNA_binding
|
84 |
169 |
7.2e-33 |
PFAM |
RFX5_DNA_bdg
|
438 |
656 |
4.29e-130 |
SMART |
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000107260
AA Change: T105I
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000102881 Gene: ENSMUSG00000005774 AA Change: T105I
Domain | Start | End | E-Value | Type |
Pfam:RFX_DNA_binding
|
88 |
167 |
5.3e-31 |
PFAM |
RFX5_DNA_bdg
|
438 |
656 |
4.29e-130 |
SMART |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000125186
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000132393
|
SMART Domains |
Protein: ENSMUSP00000117999 Gene: ENSMUSG00000005774
Domain | Start | End | E-Value | Type |
PDB:2KW3|B
|
23 |
89 |
9e-40 |
PDB |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000142708
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000137088
AA Change: T105I
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000117963 Gene: ENSMUSG00000005774 AA Change: T105I
Domain | Start | End | E-Value | Type |
Pfam:RFX_DNA_binding
|
84 |
169 |
7.2e-33 |
PFAM |
RFX5_DNA_bdg
|
438 |
656 |
4.29e-130 |
SMART |
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000142311
AA Change: T105I
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000119704 Gene: ENSMUSG00000005774 AA Change: T105I
Domain | Start | End | E-Value | Type |
Pfam:RFX_DNA_binding
|
84 |
131 |
4.1e-10 |
PFAM |
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000145031
AA Change: T105I
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000118099 Gene: ENSMUSG00000005774 AA Change: T105I
Domain | Start | End | E-Value | Type |
PDB:2KW3|B
|
23 |
89 |
9e-40 |
PDB |
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000147237
AA Change: T105I
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000118586 Gene: ENSMUSG00000005774 AA Change: T105I
Domain | Start | End | E-Value | Type |
Pfam:RFX_DNA_binding
|
84 |
169 |
8.7e-34 |
PFAM |
Pfam:Pox_D5
|
88 |
159 |
1e-7 |
PFAM |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000140294
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000148803
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000145472
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000152869
|
SMART Domains |
Protein: ENSMUSP00000121157 Gene: ENSMUSG00000005774
Domain | Start | End | E-Value | Type |
PDB:2KW3|B
|
23 |
89 |
7e-40 |
PDB |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000140331
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000144132
|
Meta Mutation Damage Score |
0.5354 |
Coding Region Coverage |
- 1x: 99.4%
- 3x: 98.8%
- 10x: 97.5%
- 20x: 95.3%
|
Validation Efficiency |
100% (68/68) |
MGI Phenotype |
PHENOTYPE: Homozygous null mice have absent or decreased expression of MHC-II complexes on antigen presenting cells, which leads to reduced numbers of CD4+ thymocytes and T cells. [provided by MGI curators]
|
Allele List at MGI |
|
Other mutations in this stock |
Total: 52 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Adgrl1 |
G |
T |
8: 84,661,279 (GRCm39) |
|
probably benign |
Het |
Adgrv1 |
C |
A |
13: 81,676,649 (GRCm39) |
D1341Y |
probably damaging |
Het |
Ahdc1 |
T |
C |
4: 132,792,827 (GRCm39) |
F1356S |
possibly damaging |
Het |
Cdk13 |
A |
G |
13: 17,895,882 (GRCm39) |
|
probably benign |
Het |
Cfhr1 |
A |
T |
1: 139,485,249 (GRCm39) |
S66T |
probably damaging |
Het |
Cldn6 |
C |
A |
17: 23,900,167 (GRCm39) |
Q44K |
probably damaging |
Het |
Cntnap5c |
T |
C |
17: 58,612,550 (GRCm39) |
V863A |
possibly damaging |
Het |
Col6a4 |
T |
A |
9: 105,944,343 (GRCm39) |
K1044* |
probably null |
Het |
Cyb561d1 |
A |
G |
3: 108,106,583 (GRCm39) |
V212A |
probably benign |
Het |
Cyp1b1 |
A |
G |
17: 80,021,275 (GRCm39) |
S156P |
probably damaging |
Het |
Dock7 |
G |
A |
4: 98,904,941 (GRCm39) |
H645Y |
probably damaging |
Het |
Dpp3 |
T |
C |
19: 4,964,682 (GRCm39) |
N542D |
probably damaging |
Het |
Fastkd3 |
C |
T |
13: 68,740,047 (GRCm39) |
|
probably benign |
Het |
Galnt10 |
T |
A |
11: 57,660,366 (GRCm39) |
V268D |
probably damaging |
Het |
Grb14 |
G |
T |
2: 64,747,631 (GRCm39) |
A10E |
probably damaging |
Het |
Grin2c |
A |
G |
11: 115,140,479 (GRCm39) |
V1213A |
probably benign |
Het |
Grip1 |
C |
T |
10: 119,846,135 (GRCm39) |
T570I |
probably damaging |
Het |
Hif1an |
T |
C |
19: 44,551,762 (GRCm39) |
Y71H |
probably benign |
Het |
Hsd17b11 |
T |
A |
5: 104,151,072 (GRCm39) |
I221L |
probably benign |
Het |
Htra1 |
A |
T |
7: 130,581,027 (GRCm39) |
|
probably benign |
Het |
Igfn1 |
T |
C |
1: 135,891,591 (GRCm39) |
E2308G |
possibly damaging |
Het |
Mapk9 |
T |
A |
11: 49,760,072 (GRCm39) |
S129T |
probably damaging |
Het |
Med22 |
T |
C |
2: 26,800,391 (GRCm39) |
T13A |
probably benign |
Het |
Miox |
C |
T |
15: 89,220,477 (GRCm39) |
L189F |
possibly damaging |
Het |
Mtus1 |
A |
T |
8: 41,446,554 (GRCm39) |
L489Q |
probably damaging |
Het |
Naprt |
G |
A |
15: 75,765,481 (GRCm39) |
P120S |
probably damaging |
Het |
Nwd1 |
C |
T |
8: 73,388,965 (GRCm39) |
P172L |
probably damaging |
Het |
Ogfod2 |
A |
G |
5: 124,250,907 (GRCm39) |
E62G |
probably null |
Het |
Or13a1 |
A |
T |
6: 116,471,361 (GRCm39) |
S264C |
probably damaging |
Het |
Or5b12b |
A |
G |
19: 12,861,910 (GRCm39) |
T222A |
probably damaging |
Het |
Or5b12b |
T |
C |
19: 12,861,443 (GRCm39) |
L66P |
probably damaging |
Het |
Palm |
A |
C |
10: 79,655,327 (GRCm39) |
T362P |
probably benign |
Het |
Pcare |
T |
G |
17: 72,056,509 (GRCm39) |
H1056P |
probably benign |
Het |
Pcdh8 |
T |
C |
14: 80,007,400 (GRCm39) |
T388A |
probably benign |
Het |
Pclo |
A |
G |
5: 14,725,332 (GRCm39) |
I1397V |
unknown |
Het |
Per1 |
A |
G |
11: 68,992,027 (GRCm39) |
E127G |
probably damaging |
Het |
Plekha1 |
T |
C |
7: 130,502,353 (GRCm39) |
V30A |
possibly damaging |
Het |
Pramel24 |
A |
T |
4: 143,454,622 (GRCm39) |
T307S |
probably benign |
Het |
Rab26 |
A |
G |
17: 24,746,940 (GRCm39) |
|
probably benign |
Het |
Rasal2 |
T |
C |
1: 156,984,750 (GRCm39) |
D999G |
possibly damaging |
Het |
Rrp1b |
T |
C |
17: 32,279,369 (GRCm39) |
S677P |
probably damaging |
Het |
Scaf4 |
G |
A |
16: 90,046,582 (GRCm39) |
P485S |
unknown |
Het |
Scn5a |
A |
T |
9: 119,368,706 (GRCm39) |
M273K |
probably damaging |
Het |
Sec22a |
C |
T |
16: 35,181,926 (GRCm39) |
|
probably null |
Het |
Slc10a6 |
C |
A |
5: 103,760,315 (GRCm39) |
V227F |
possibly damaging |
Het |
Slc39a3 |
C |
G |
10: 80,869,565 (GRCm39) |
E31Q |
probably benign |
Het |
Spsb1 |
C |
T |
4: 149,991,374 (GRCm39) |
V65I |
probably benign |
Het |
Tdrd7 |
T |
A |
4: 46,016,879 (GRCm39) |
M673K |
probably benign |
Het |
Trim8 |
C |
A |
19: 46,503,532 (GRCm39) |
S361R |
possibly damaging |
Het |
Ucp1 |
T |
A |
8: 84,021,936 (GRCm39) |
M256K |
possibly damaging |
Het |
Vmn1r46 |
A |
T |
6: 89,953,946 (GRCm39) |
D265V |
probably damaging |
Het |
Zbtb5 |
T |
C |
4: 44,993,787 (GRCm39) |
I532M |
probably damaging |
Het |
|
Other mutations in Rfx5 |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
IGL01459:Rfx5
|
APN |
3 |
94,865,086 (GRCm39) |
unclassified |
probably benign |
|
IGL01478:Rfx5
|
APN |
3 |
94,865,751 (GRCm39) |
missense |
possibly damaging |
0.88 |
IGL02061:Rfx5
|
APN |
3 |
94,865,792 (GRCm39) |
missense |
probably benign |
0.03 |
IGL02152:Rfx5
|
APN |
3 |
94,864,493 (GRCm39) |
missense |
probably damaging |
1.00 |
IGL03395:Rfx5
|
APN |
3 |
94,865,113 (GRCm39) |
nonsense |
probably null |
|
chip
|
UTSW |
3 |
94,863,666 (GRCm39) |
missense |
probably damaging |
1.00 |
nonplussed
|
UTSW |
3 |
94,866,272 (GRCm39) |
missense |
unknown |
|
shrunken
|
UTSW |
3 |
94,862,454 (GRCm39) |
missense |
probably damaging |
1.00 |
R0098:Rfx5
|
UTSW |
3 |
94,865,679 (GRCm39) |
missense |
probably damaging |
1.00 |
R0098:Rfx5
|
UTSW |
3 |
94,865,679 (GRCm39) |
missense |
probably damaging |
1.00 |
R0505:Rfx5
|
UTSW |
3 |
94,863,666 (GRCm39) |
missense |
probably damaging |
1.00 |
R1342:Rfx5
|
UTSW |
3 |
94,865,723 (GRCm39) |
missense |
probably benign |
0.09 |
R1460:Rfx5
|
UTSW |
3 |
94,863,636 (GRCm39) |
missense |
probably damaging |
1.00 |
R1466:Rfx5
|
UTSW |
3 |
94,863,614 (GRCm39) |
missense |
probably damaging |
1.00 |
R1466:Rfx5
|
UTSW |
3 |
94,863,614 (GRCm39) |
missense |
probably damaging |
1.00 |
R1972:Rfx5
|
UTSW |
3 |
94,864,603 (GRCm39) |
missense |
probably damaging |
1.00 |
R2173:Rfx5
|
UTSW |
3 |
94,864,027 (GRCm39) |
splice site |
probably null |
|
R4808:Rfx5
|
UTSW |
3 |
94,865,591 (GRCm39) |
missense |
probably benign |
0.03 |
R4993:Rfx5
|
UTSW |
3 |
94,863,126 (GRCm39) |
missense |
probably benign |
0.27 |
R4996:Rfx5
|
UTSW |
3 |
94,863,126 (GRCm39) |
missense |
probably benign |
0.27 |
R5104:Rfx5
|
UTSW |
3 |
94,862,451 (GRCm39) |
missense |
probably benign |
0.35 |
R5912:Rfx5
|
UTSW |
3 |
94,866,029 (GRCm39) |
unclassified |
probably benign |
|
R7097:Rfx5
|
UTSW |
3 |
94,863,850 (GRCm39) |
missense |
probably damaging |
1.00 |
R7186:Rfx5
|
UTSW |
3 |
94,865,659 (GRCm39) |
missense |
probably benign |
0.01 |
R7194:Rfx5
|
UTSW |
3 |
94,862,454 (GRCm39) |
missense |
probably damaging |
1.00 |
R7202:Rfx5
|
UTSW |
3 |
94,866,272 (GRCm39) |
missense |
unknown |
|
R7203:Rfx5
|
UTSW |
3 |
94,866,187 (GRCm39) |
missense |
unknown |
|
R7374:Rfx5
|
UTSW |
3 |
94,866,053 (GRCm39) |
missense |
unknown |
|
R7375:Rfx5
|
UTSW |
3 |
94,866,053 (GRCm39) |
missense |
unknown |
|
R8919:Rfx5
|
UTSW |
3 |
94,864,475 (GRCm39) |
missense |
probably damaging |
1.00 |
R9562:Rfx5
|
UTSW |
3 |
94,866,639 (GRCm39) |
missense |
unknown |
|
RF061:Rfx5
|
UTSW |
3 |
94,863,070 (GRCm39) |
missense |
probably damaging |
1.00 |
Z1176:Rfx5
|
UTSW |
3 |
94,863,126 (GRCm39) |
missense |
probably benign |
0.27 |
|
Predicted Primers |
PCR Primer
(F):5'- GGGACAAACTGATTCGATCTGGCAC -3'
(R):5'- TCCAGGCAATGGTGGCATGGATAC -3'
Sequencing Primer
(F):5'- GATTCGATCTGGCACCATCAAAG -3'
(R):5'- GTCCTAATCTCTGGGTCAAGGATAC -3'
|
Posted On |
2013-07-30 |